Re: GPU-based deconvolution

Posted by Brian Northan on
URL: http://confocal-microscopy-list.275.s1.nabble.com/GPU-based-deconvolution-tp7582498p7582518.html

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Hi Sergey

COSMOS is a legacy software, but the only that
> supports PSF generation according to Haeberle and Török models.
> I'd like to
> speedup PSF generation, 1hr for 256*256*40 is too much.
>

One hour is for sure too much.  Did you try the Gibson Lanni model??  It
should be faster. I used the COSMOS PSF generation code for another project
and have a simple hack that makes it faster.   Do you compile the code or
just use their executables??  My copy generates a 256 by 256 by 40 PSF in
under 10 seconds.

If compiling the code you can do the following.  They use oversampling when
generating PSFs.   Under the main Cosm code tree there is a file
/psf/psf/psf.cxx.   There is a function in this file called 'evaluate'.
The first line creates a 'radialPsf'.   There is an additional optional
variable you can pass to the 'radialPsf' constructor that specifies the
oversampling factor (default value is 32).  If you pass 2 the code will run
faster and the result won't change too much.

(You might want to test on a bead image or phantom sample to confirm this)

Brian


On Thu, Aug 14, 2014 at 8:57 AM, George McNamara <[hidden email]>
wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi Sergey,
>
> One great point Manish emphasized to me is that anytime we are using
> FFT's, to give the FFT routines data with power of two dimensions. So,
> instead of 256*256*40, you would be better off with 256*256*32, and might
> be better off with 256*256*64.
>
> If COSMOS is no longer being developed by Prof. Preza, all the more reason
> for you to adopt it! It is using a GNU General Public License,
> http://cirl.memphis.edu/cosmos_faqs.php
>
> Likewise the Clarity deconvolution library at UNC is no longer being
> developed, consider taking over that.
>
> Adam Hoppe told me several months ago that he is continuing to work on
> 3DFSR, so consider contacting him at http://www.sdstate.edu/chem/
> faculty/adam-hoppe/
>
> I forgot to mention in yesterday's email the BoaDeconvolution -- already
> Parallel Deconvolution --  at
> http://pawliczek.net.pl/deconvolution/
> http://onlinelibrary.wiley.com/doi/10.1002/jemt.20773/abstract
>
> I've previously posted to the listserv more on GPU (and Xeon, Xeon Phi,
> Knights Landing proposal).
>
> best wishes,
>
> George
>
>
>
> On 8/14/2014 4:14 AM, Sergey Tauger wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> Post images on http://www.imgur.com and include the link in your posting.
>> *****
>>
>> George,
>>
>> Thank you for useful links. I'm going to write my own deconvolution
>> software or
>> contribute to existing. At the moment I use DeconvolutionLab and COSMOS
>> for
>> PSF generation. To my regret,  COSMOS is a legacy software, but the only
>> that
>> supports PSF generation according to Haeberle and T&#246;r&#246;k models.
>> I'd like to
>> speedup PSF generation, 1hr for 256*256*40 is too much.
>>
>> I do not overestimate my programming skills, so I'd better use a existing
>> GPU-
>> based PSF generation software as a "best practice" guide than writing my
>> own
>> implementation from scratch. If I succeed in speeding up PSF generation,
>> I'll post
>> a link to github in this thread.
>>
>> Best,
>> Sergey
>>
>>
>>
>
>
> --
>
>
>
> George McNamara, Ph.D.
> Single Cells Analyst
> L.J.N. Cooper Lab
> University of Texas M.D. Anderson Cancer Center
> Houston, TX 77054
> Tattletales http://works.bepress.com/gmcnamara/42
>